Variant report

Variant	rs10060446
Chromosome Location	chr5:177562251-177562252
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:177562117-177562454	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr5:177562108-177562563	GM12892	blood:	n/a	n/a
3	POLR2A	chr5:177562105-177562451	K562	blood:	n/a	n/a
4	POLR2A	chr5:177562071-177563164	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr5:177562234-177562874	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr5:177562172-177562400	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr5:177561918-177566392	K562	blood:	n/a	n/a
8	POLR2A	chr5:177562201-177562311	A549	lung:	n/a	n/a
9	POLR2A	chr5:177562088-177562402	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:177560352..177564718-chr5:177565737..177570754,8	K562	blood:
2	chr5:177554438..177556086-chr5:177561391..177563807,2	K562	blood:
3	chr3:161088076..161090041-chr5:177561161..177563994,2	MCF-7	breast:
4	chr5:176852652..176854366-chr5:177560373..177562454,2	K562	blood:
5	chr5:177561649..177563413-chr5:177634433..177636302,2	K562	blood:
6	chr5:177538943..177540925-chr5:177562245..177563992,2	K562	blood:
7	chr5:177554586..177557949-chr5:177561501..177564806,6	K562	blood:

No data

Variant related genes	Relation type
RMND5B	TF binding region
ENSG00000145911	Chromatin interaction
ENSG00000145916	Chromatin interaction
ENSG00000198055	Chromatin interaction
ENSG00000196542	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10035478	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10040895	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10074810	0.81[ASN][1000 genomes]
rs12655707	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13155699	0.87[ASN][1000 genomes]
rs13163671	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13165989	0.90[ASN][1000 genomes]
rs13175750	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13180226	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13185017	0.81[ASN][1000 genomes]
rs13185763	0.88[ASN][1000 genomes]
rs13436876	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34093388	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34343747	0.88[ASN][1000 genomes]
rs34353050	0.90[ASN][1000 genomes]
rs35027513	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35433113	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35598853	0.89[ASN][1000 genomes]
rs36087128	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs36090803	0.88[ASN][1000 genomes]
rs3812073	0.93[ASN][1000 genomes]
rs3812074	0.80[ASN][1000 genomes]
rs3812075	0.82[ASN][1000 genomes]
rs3812077	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3812079	0.80[ASN][1000 genomes]
rs3812080	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3924305	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4637566	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56351116	0.81[ASN][1000 genomes]
rs6601217	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6873523	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6876480	0.81[AMR][1000 genomes]
rs6886057	0.82[ASN][1000 genomes]
rs7379278	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs7380947	0.80[AFR][1000 genomes]
rs7443359	0.83[ASN][1000 genomes]
rs7447860	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7448252	0.83[ASN][1000 genomes]
rs7716409	0.87[ASN][1000 genomes]
rs7716860	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7733574	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030383	chr5:177310325-177571254	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
3	nsv1021198	chr5:177386267-177611648	Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
5	nsv462567	chr5:177505021-177572927	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv471058	chr5:177505021-177572927	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv600392	chr5:177505021-177572927	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv1019404	chr5:177507080-177859089	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	126 gene(s)	inside rSNPs	diseases
9	nsv883190	chr5:177532201-177620189	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
10	nsv883192	chr5:177535370-177564346	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
11	nsv600394	chr5:177549491-177608195	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177558800-177569600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:177558800-177576800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr5:177559000-177562400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr5:177559000-177562400	Weak transcription	Osteobl	bone
5	chr5:177559000-177562600	Weak transcription	Fetal Intestine Large	intestine
6	chr5:177559000-177562800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr5:177559000-177562800	Weak transcription	NH-A	brain
8	chr5:177559000-177563000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr5:177559000-177565000	Weak transcription	Brain Angular Gyrus	brain
10	chr5:177559000-177569000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr5:177559000-177569200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr5:177559000-177569200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr5:177559000-177569200	Weak transcription	Gastric	stomach
14	chr5:177559000-177569200	Weak transcription	HSMM	muscle
15	chr5:177559000-177569400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr5:177559000-177569600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr5:177559000-177569800	Weak transcription	HUVEC	blood vessel
18	chr5:177559000-177569800	Weak transcription	NHDF-Ad	bronchial
19	chr5:177559000-177570600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr5:177559000-177572800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:177559000-177572800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr5:177559000-177574000	Weak transcription	Small Intestine	intestine
23	chr5:177559000-177580000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr5:177559000-177580000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr5:177559200-177562600	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr5:177559200-177562800	Weak transcription	NHLF	lung
27	chr5:177559200-177563200	Weak transcription	NHEK	skin
28	chr5:177559200-177563400	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr5:177559200-177563800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr5:177559200-177563800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr5:177559200-177565000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr5:177559200-177565000	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr5:177559200-177568800	Weak transcription	HSMMtube	muscle
34	chr5:177559200-177569600	Weak transcription	HMEC	breast
35	chr5:177559200-177569800	Weak transcription	Colon Smooth Muscle	Colon
36	chr5:177559200-177570400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr5:177559200-177573000	Weak transcription	Psoas Muscle	Psoas
38	chr5:177559200-177573200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr5:177559200-177579800	Weak transcription	Right Atrium	heart
40	chr5:177559400-177570400	Weak transcription	Fetal Heart	heart
41	chr5:177559600-177562400	Weak transcription	Stomach Mucosa	stomach
42	chr5:177559600-177562400	Weak transcription	HepG2	liver
43	chr5:177559600-177562600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr5:177559600-177562600	Weak transcription	GM12878-XiMat	blood
45	chr5:177559600-177567000	Weak transcription	Fetal Kidney	kidney
46	chr5:177559600-177569000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr5:177559600-177569400	Weak transcription	Hela-S3	cervix
48	chr5:177559600-177569800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr5:177559800-177577600	Weak transcription	Fetal Brain Male	brain
50	chr5:177560200-177566000	Strong transcription	Brain Germinal Matrix	brain

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